Zinc in PDB 8eip: Crystal Structure of Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg

The structure of Crystal Structure of Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg, PDB code: 8eip was solved by I.Sharon, T.M.Schmeing, with X-Ray Crystallography technique. A brief refinement statistics is given in the table below:

Resolution Low / High (Å)	49.04 / 2.24
Space group	C 1 2 1
Cell size a, b, c (Å), α, β, γ (°)	151.529, 126.648, 109.516, 90, 130.39, 90
R / Rfree (%)	22.6 / 25.8

The structure of Crystal Structure of Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg also contains other interesting chemical elements:

Manganese

(Mn)

4 atoms

The binding sites of Zinc atom in the Crystal Structure of Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg (pdb code 8eip). This binding sites where shown within 5.0 Angstroms radius around Zinc atom.
In total 4 binding sites of Zinc where determined in the Crystal Structure of Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg, PDB code: 8eip:
Jump to Zinc binding site number: 1; 2; 3; 4;

Zinc binding site 1 out of 4 in the Crystal Structure of Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 1 of Crystal Structure of Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg within 5.0Å range: probe atom residue distance (Å) B Occ A:Zn402 b:68.2 occ:1.00 OD1 A:7ID401 1.7 64.0 1.0 ND1 A:HIS179 2.0 45.5 1.0 ND1 A:HIS50 2.3 40.5 1.0 OE1 A:GLU53 2.5 41.6 1.0 OE2 A:GLU53 2.8 41.2 1.0 CE1 A:HIS179 2.9 41.6 1.0 CG A:7ID401 2.9 61.7 1.0 CD A:GLU53 3.0 43.2 1.0 CE1 A:HIS50 3.0 40.7 1.0 CG A:HIS179 3.1 40.9 1.0 OX2 A:7ID401 3.4 62.6 1.0 CG A:HIS50 3.4 43.5 1.0 CB A:HIS179 3.5 35.9 1.0 CO2 A:7ID401 3.7 70.1 1.0 N2 A:7ID401 3.7 69.0 1.0 CA2 A:7ID401 3.8 63.1 1.0 CB A:HIS50 3.9 34.4 1.0 NE2 A:HIS179 4.0 48.9 1.0 O A:HOH558 4.0 37.8 1.0 CB A:7ID401 4.0 67.5 1.0 O A:ALA180 4.1 43.2 1.0 CD2 A:HIS179 4.1 42.7 1.0 NH1 A:ARG102 4.2 53.0 1.0 NE2 A:HIS50 4.2 45.2 1.0 CA A:HIS179 4.4 38.5 1.0 CG A:GLU53 4.4 42.8 1.0 CD2 A:HIS50 4.5 38.4 1.0 O2 A:7ID401 4.5 75.4 1.0 N A:ALA180 4.5 39.2 1.0 O A:HOH518 4.9 47.5 1.0 CA A:7ID401 4.9 64.8 1.0

Zinc binding site 2 out of 4 in the Crystal Structure of Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 2 of Crystal Structure of Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg within 5.0Å range: probe atom residue distance (Å) B Occ B:Zn402 b:64.9 occ:1.00 ND1 B:HIS179 1.9 53.9 1.0 OD1 B:7ID401 2.0 56.6 1.0 ND1 B:HIS50 2.4 40.5 1.0 OE1 B:GLU53 2.4 40.8 1.0 CE1 B:HIS179 2.7 44.9 1.0 OE2 B:GLU53 2.9 34.0 1.0 CG B:HIS179 2.9 42.9 1.0 CD B:GLU53 3.0 47.4 1.0 O2 B:7ID401 3.1 66.2 1.0 CE1 B:HIS50 3.1 33.6 1.0 CG B:7ID401 3.2 62.1 1.0 CB B:HIS179 3.4 38.1 1.0 CO2 B:7ID401 3.4 63.1 1.0 CG B:HIS50 3.5 38.7 1.0 CA2 B:7ID401 3.8 57.3 1.0 NE2 B:HIS179 3.9 43.7 1.0 CB B:HIS50 3.9 30.0 1.0 N2 B:7ID401 3.9 59.0 1.0 O B:HOH614 4.0 39.5 1.0 CD2 B:HIS179 4.0 47.2 1.0 OX2 B:7ID401 4.1 71.1 1.0 O B:ALA180 4.1 40.2 1.0 CA B:HIS179 4.3 41.3 1.0 NE2 B:HIS50 4.4 40.7 1.0 CB B:7ID401 4.4 55.6 1.0 NH1 B:ARG102 4.4 46.7 1.0 CG B:GLU53 4.4 31.4 1.0 N B:ALA180 4.5 39.2 1.0 CD2 B:HIS50 4.5 40.5 1.0 C B:HIS179 5.0 42.6 1.0

Zinc binding site 3 out of 4 in the Crystal Structure of Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 3 of Crystal Structure of Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg within 5.0Å range: probe atom residue distance (Å) B Occ C:Zn402 b:74.8 occ:1.00 OD1 C:7ID401 1.8 66.8 1.0 ND1 C:HIS179 2.0 53.9 1.0 ND1 C:HIS50 2.2 45.6 1.0 OE1 C:GLU53 2.4 47.6 1.0 OE2 C:GLU53 2.9 47.0 1.0 CE1 C:HIS179 2.9 45.8 1.0 CE1 C:HIS50 2.9 43.9 1.0 CG C:7ID401 2.9 63.8 1.0 CD C:GLU53 2.9 46.5 1.0 CG C:HIS179 3.0 44.4 1.0 CG C:HIS50 3.3 45.3 1.0 CB C:HIS179 3.4 42.4 1.0 OX2 C:7ID401 3.4 66.4 1.0 CA2 C:7ID401 3.7 61.4 1.0 CO2 C:7ID401 3.7 69.5 1.0 N2 C:7ID401 3.7 57.7 1.0 CB C:HIS50 3.8 44.5 1.0 NE2 C:HIS179 4.0 50.1 1.0 CB C:7ID401 4.0 63.6 1.0 CD2 C:HIS179 4.1 48.7 1.0 O C:ALA180 4.1 44.9 1.0 NE2 C:HIS50 4.1 44.1 1.0 O C:HOH551 4.2 46.5 1.0 NH1 C:ARG102 4.3 57.5 1.0 CA C:HIS179 4.3 44.2 1.0 CD2 C:HIS50 4.3 51.3 1.0 CG C:GLU53 4.4 46.7 1.0 N C:ALA180 4.4 37.2 1.0 O2 C:7ID401 4.6 67.9 1.0 CA C:7ID401 4.7 61.6 1.0 O C:HOH546 4.9 42.5 1.0 C C:HIS179 5.0 39.2 1.0

Zinc binding site 4 out of 4 in the Crystal Structure of Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg


Mono view


Stereo pair view

A full contact list of Zinc with other atoms in the Zn binding site number 4 of Crystal Structure of Cyanophycin Dipeptide Hydrolase Cphz E251A From Acinetobacter Baylyi DSM587 in Complex with Beta-Asp-Arg within 5.0Å range: probe atom residue distance (Å) B Occ D:Zn402 b:72.6 occ:1.00 OD1 D:7ID401 1.7 80.6 1.0 ND1 D:HIS179 2.1 52.7 1.0 ND1 D:HIS50 2.3 52.2 1.0 OE1 D:GLU53 2.3 47.0 1.0 OE2 D:GLU53 2.7 48.7 1.0 CD D:GLU53 2.8 54.7 1.0 CG D:7ID401 3.0 70.7 1.0 CE1 D:HIS179 3.0 54.9 1.0 CG D:HIS179 3.1 50.4 1.0 CE1 D:HIS50 3.1 46.6 1.0 O2 D:7ID401 3.3 69.1 1.0 CG D:HIS50 3.4 46.6 1.0 CB D:HIS179 3.5 50.7 1.0 CO2 D:7ID401 3.5 66.4 1.0 CB D:HIS50 3.8 38.1 1.0 N2 D:7ID401 3.8 70.7 1.0 CA2 D:7ID401 3.9 64.0 1.0 O D:ALA180 3.9 46.7 1.0 O D:HOH544 3.9 44.8 1.0 CB D:7ID401 4.0 59.1 1.0 OX2 D:7ID401 4.0 76.5 1.0 NE2 D:HIS179 4.1 52.7 1.0 NH1 D:ARG102 4.2 54.9 1.0 CD2 D:HIS179 4.2 52.2 1.0 CG D:GLU53 4.3 47.2 1.0 NE2 D:HIS50 4.3 59.2 1.0 CA D:HIS179 4.4 54.7 1.0 N D:ALA180 4.4 51.1 1.0 CD2 D:HIS50 4.5 48.8 1.0 CA D:7ID401 4.7 66.7 1.0 C D:HIS179 5.0 48.5 1.0 CB D:GLU53 5.0 42.7 1.0

I.Sharon, G.A.Mckay, D.Nguyen, T.M.Schmeing. Discovery of Cyanophycin Dipeptide Hydrolase Enzymes Suggests Widespread Utility of the Natural Biopolymer Cyanophycin. Proc.Natl.Acad.Sci.Usa V. 120 47120 2023.
ISSN: ESSN 1091-6490
PubMed: 36800389
DOI: 10.1073/PNAS.2216547120